A next-generation Integrative Genomics Viewer for biomedical and cancer research.

描述（由申请人提供）：在数据获取新技术的推动下，包含大量样本的整合基因组研究有望彻底改变我们研究癌症和其他疾病的方式，并为新的治疗方案绘制道路。它们需要对多种类型的基因组数据进行高通量生成和分析。为了应对这一挑战，在与终端用户的积极合作下，我们开发了一款广泛适用的整合基因组学查看器（IGV）。IGV是一种高性能、用户友好的工具，被世界各地成千上万的研究人员用于大型综合基因组数据集的交互式探索。该项目的目标是开发下一代IGV，以便从当前和未来生物医学研究人员面临的基因组数据爆炸中提取生物学知识。具体来说，我们计划通过增加分析驱动的导航、新的互补非基因组视图、来自多个研究的大量样本的多层次表示以及丰富的协作环境，将IGV提升到一个新的水平。目的1。通过智能的、分析驱动的导航，结合新的功能、结构和多层次视图，利用IGV实现对大规模、多研究数据集的直观探索。目标2。提供对基因组数据集的注释和分享见解的能力，通过IGV提高研究合作的速度和便利性。目标3。为开发人员提供外联服务，并为IGV软件和用户提供持续的维护和支持。我们在软件工程方面有丰富的经验，包括开发和分发被全世界成千上万的科学家使用的软件。我们将继续以用户为导向的开发方法，与许多大型基因组项目密切合作，如癌症基因组图谱、国际癌症联盟、1000基因组和ENCODE，以及许多单个研究者的研究。IGV目前的成功、灵活的架构以及我们支持外部开发的计划，使我们能够很好地实现我们的目标，进一步转变数据可视化，实现并加速生物医学发现的步伐。

DESCRIPTION (provided by applicant): Driven by new technologies for data acquisition, integrative genomic studies comprising large numbers of samples are poised to revolutionize the way we approach the study of cancer and other diseases and chart the way to novel treatment regimens. They require the high-throughput generation and analysis of multiple types of genomic data. To address this challenge, and in active collaboration with end users, we developed a broadly applicable Integrative Genomics Viewer (IGV). IGV is a high-performance, user-friendly tool used by thousands of investigators world-wide for the interactive exploration of large, integrated genomic datasets. The goal of this project is to develop the next-generation of the IGV for extracting biological knowledge from the explosion of genomic data facing biomedical researchers both today and in the future. Specifically, we plan to take IGV to the next level with the addition of analysis-driven navigation, new complementary non-genomic views, multi-level representations of large numbers of samples from multiple studies, and a rich collaboration environment. Aim 1. To enable intuitive exploration of large-scale, multi-study datasets with IGV through intelligent, analysis-driven navigation combined with new functional, structural, and multi-level views. Aim 2. To provide the capability to annotate views and share insights on genomic datasets to enhance the speed and ease of research collaborations via IGV. Aim 3. To provide developer outreach and continued maintenance and support of the IGV software and users. We have extensive experience in software engineering, including the development and distribution of software used by tens of thousands of scientists world-wide. We will continue our user-driven development approach working closely with many large genomics projects like The Cancer Genome Atlas, the International Cancer Consortium, the 1000 Genomes, and ENCODE, as well as numerous single-investigator studies. IGV's current success, flexible architecture, and our plan to support external development make us well poised to accomplish our aims to further transform data visualization and enable and accelerate the pace of biomedical discovery. PUBLIC HEALTH RELEVANCE: We propose to develop the next-generation of the Integrative Genomics Viewer (IGV) to support biomedical research through the interactive and collaborative visualization and exploration of genomic data. Given the enormous amount of data generated by studies today, visualization is often a key element in gaining insight into the genomic basis and mechanisms of disease. These insights will help to develop hypotheses for further study and point the way to new therapeutic targets.